In the manuscript, entitled "CNVpytor: a tool for CNV/CNA detection and analysis from read depth and alle imbalance in whole genome sequencing", Suvakov et al., present an extension of CNVnator, a popular CNV caller they previously developed, in Python with significant calculating speed improvement and a newly implemented CNV detection algorithm based on B-allele frequency. Although the current development is based on the original CNVnator, I think the new development in CNVpytor is certainly significant and important. This is not only because of the significant performance improvement and new features in the CNVpytor as pointed out already by the authors, but also because, in my opinion, it is important to re-engineer the classical bioinformatic tools, e.g., CNVnator (developed 10 years ago), with up-to-date programming languages and trim them to work efficiently under modern computational hardware and OS environment. This will save substantial amount of time and effort for their users, and therefore, be significantly useful to the field of research.

I have two minor suggestions: 1. What is the resolution of CNVpytor for detecting CNAs? This information would be very useful for its users. I suggest the authors at least can provide a comment on the maximum resolution that they recommend.

1. What is the minimum sequencing depth required by CNVpytor, and can it be applied to other types of DNA sequencing data, e.g., whole-exome sequencing? Same as the above, I think these information may also be very useful.

Declaration of competing interests Please complete a declaration of competing interests, considering the following questions: Have you in the past five years received reimbursements, fees, funding, or salary from an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold any stocks or shares in an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold or are you currently applying for any patents relating to the content of the manuscript? Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript? Do you have any other financial competing interests? Do you have any non-financial competing interests in relation to this paper? If you can answer no to all of the above, write 'I declare that I have no competing interests' below. If your reply is yes to any, please give details below.

I am a co-founder of SingulOmics Corp. It is a biotech company at New York City, USA. However, I do not have any financial competing interests in relation to this specific paper.

I agree to the open peer review policy of the journal. I understand that my name will be included on my report to the authors and, if the manuscript is accepted for publication, my named report including any attachments I upload will be posted on the website along with the authors' responses. I agree for my report to be made available under an Open Access Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments which I do not wish to be included in my named report can be included as confidential comments to the editors, which will not be published. I agree to the open peer review policy of the journal.

Authors' response to reviews: (https://drive.google.com/file/d/1MdGSlpFZ_D8SfYxHFXEzsG5jahP3E1KQ/view?usp=sharing)

The main point of the manuscript is about an update of an existing (but important) software. The updates include new platform (python), new interface (web plugin) and functionality (merging variants from multiple samples and filtering), which are all clearly listed in the new Supplemental Table 2 with a comparison with many other existing software tools including its original tool (CNVnator). The updates also include performance improvement, which is parallel processing. Although parallel processing cannot improve accuracy, it is a very important feature because it will save its users significant amount of time.

The "in depth" comparison mentioned in the discussion between one of the reviewers and the authors is about accuracy - which I agree with the authors that it is the same as the original tool as expected. However, it is clear that the bullet point of the manuscript is about all the other aspect of updates (as described above), not its accuracy. So, in my opinion, the authors have provided a detailed comparison with existing tools in the Suppl. Table 2.

So, I think the current manuscript fits exactly the criteria of the journal's Technical Note, and fully support its publication.

Declaration of competing interests Please complete a declaration of competing interests, considering the following questions: Have you in the past five years received reimbursements, fees, funding, or salary from an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold any stocks or shares in an organisation that may in any way gain or lose financially from the publication of this manuscript, either now or in the future? Do you hold or are you currently applying for any patents relating to the content of the manuscript? Have you received reimbursements, fees, funding, or salary from an organization that holds or has applied for patents relating to the content of the manuscript? Do you have any other financial competing interests? Do you have any non-financial competing interests in relation to this paper? If you can answer no to all of the above, write 'I declare that I have no competing interests' below. If your reply is yes to any, please give details below.

I am a co-founder of SingulOmics Corp. It is a biotech company at New York City, USA. However, I do not have any financial competing interests in relation to this specific paper.

I agree to the open peer review policy of the journal. I understand that my name will be included on my report to the authors and, if the manuscript is accepted for publication, my named report including any attachments I upload will be posted on the website along with the authors' responses. I agree for my report to be made available under an Open Access Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any comments which I do not wish to be included in my named report can be included as confidential comments to the editors, which will not be published. I agree to the open peer review policy of the journal.

Authors' response to reviews: (https://drive.google.com/file/d/17dUC_O5RQCs3JPWp6sLjlWM8-KXwQVRR/view?usp=sharing)